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Microbes & Immunity Brachyspira pilosicoli novel outer membrane proteins

Table 2. (Continued)
Functional categories a Subtypes Protein accession number Locus identifier Protein name a
WP_013244610.1 BP951000_RS08300 Tia invasion determinant
WP_013244059.1 BP951000_RS05490 Tia invasion determinant
WP_228369485.1 BP951000_RS08295 Tia invasion determinant
WP_013243225.1 BP951000_RS01280 Serpentine receptor domain-
containing protein
WP_013244338.1 BP951000_RS06930 Serpentine receptor domain-
containing protein
WP_013243037.1 BP951000_RS00365 Serpentine receptor domain-
containing protein
Immune evasion WP_013244610.1 BP951000_RS08300 d Tia invasion determinant
proteins WP_013242999.1 BP951000_RS00185 Hypothetical protein
WP_228369485.1 BP951000_RS08295 d Tia invasion determinant
Signal transduction Receptor-like WP_181893515.1 BP951000_RS01590 Hypothetical protein
OMPs WP_013243193.1 BP951000_RS01125 d CsgG/HfaB family protein
Enzymatic functions Lipases WP_013243647.1 BP951000_RS03405 Hypothetical protein
Notes: Protein names follow annotations in the National Center for Biotechnology Information and UniProt databases, retrieved using protein
a
accession numbers (accessed on March 28, 2024). Functional categories were assigned based on consensus predictions from structure- and sequence-
b
based annotation tools (Table S3). As serpentine receptors, or G-protein coupled receptors, are absent in prokaryotes and all tools predicted
c
transmembrane β-barrel structures rather than α-helices, these proteins are likely misannotated as serpentine receptor proteins in UniProt. These
d
proteins were predicted to possess dual roles.
Abbreviations: DUF: Domain of unknown function; OM: Outer membrane; OMBB: Outer membrane β-barrel; OMP: Outer membrane protein; Trep:
transcriptional regulating protein.
(BP951000_RS02055, BP951000_RS02055, BP951000_ Brachyspira pilosicoli BamA consists of 16 antiparallel
RS07540, BP951000_RS01125, BP951000_RS00180, β-strands, with a characteristic lateral gate between
BP951000_RS03440, and BP951000_RS04880), and three strands 1 and 16. A structural homology search using
TolC family proteins (BP951000_RS05600, BP951000_ the DALI server revealed the closest match with
RS09000, and BP951000_RS06235) (Table 1). Out of the BamA of Escherichia coli O157:H7 (PDB ID: 7NRE)
seven eight-stranded β-barrel proteins, five are annotated (Tables 2 and S3). The consensus predictions from other
as serpentine receptor (SR) domain-containing proteins annotation tools (Foldseek, PANNZER, and eggNOG-
(BP951000_RS02055, BP951000_RS02055, BP951000_ mapper) validated the functional annotation of BamA in
RS07540, BP951000_RS00180, and BP951000_RS04880). B. pilosicoli (Table S3).

3.2.1.1. BP951000_RS05730 Sequence comparison of BP951000_RS05730 across
BP951000_RS05730 is annotated as BamA in B. pilosicoli nine strains of B. pilosicoli revealed five variations (D60,
strain 95/1000. BamA, along with BamB, BamC, BamD, A184, V465, A467, and F512) (Tables 3 and S4). When
and BamE, forms the β-barrel assembly machinery mapped onto the structural model, V465, A467, and F512
complex, which is involved in the assembly and insertion were present in the β-barrel transmembrane (TM) domain,
60
of β-barrel proteins into the OM. BP951000_RS05730 is whereas D60 and V184 were located in the periplasmic
identified as an essential protein in the DEG database. Its region of the protein (Tables 3 and S4).
structural model exhibits a characteristic BamA bipartite 3.2.1.2. BP951000_RS10215
structure, consisting of a periplasmic N-terminal region
and a C-terminal b-barrel domain (Figure 2A). The BP951000_RS10215 is annotated as a hypothetical protein
N-terminal segment contains five polypeptide transport- in NCBI. However, it is annotated as a variable surface
associated (POTRA) domains (P1–P5), each comprising protein (Vsp), specifically VspE, in the UniProt database.
a characteristic β1-α1-α2-β2-β3 motif. In other well- Vsps are OMPs identified in Brachyspira hyodysenteriae and
characterized BamA proteins, these domains form a Mycoplasma bovis, and are used by these pathogenic bacteria
scaffold for the binding of BamB, BamC, BamD, and BamE to adapt to host conditions and enhance colonization. 62,63
proteins, and facilitate the folding of OMPs. 61 These proteins can undergo reversible on/off expression

Volume 2 Issue 4 (2025) 87 doi: 10.36922/MI025230050